By simultaneous analysis of the on-time distribution and autocorrelation function of a single working cholesterol oxidase enzyme, a diffusional model reveals the coupling of conformation change with enzyme action. Activesite oxidation induces a conformational change that opens the path for substrate entry. Its binding, in turn, induces the reverse protein relaxation process, which tightens the ...

Transitions between metastable conformations of a dipeptide are investigated using classical molecular dynamics simulation with explicit water molecules. The distribution of the surrounding water at different moments before the transitions and the dynamical correlations of water with the peptide's configurational motions indicate that the water molecules represent an integral part of the molecu...

DNA repeat domains can form ensembles of canonical and noncanonical states, including stable and metastable DNA secondary structures. Such sequence-induced structural diversity creates complex conformational landscapes for DNA processing pathways, including those triplet expansion events that accompany replication, recombination, and/or repair. Here we demonstrate further levels of conformation...

Ligation of short DNA fragments results in the formation of linear and circular multimers of various lengths. The distribution of products in such a reaction is often used to evaluate fragment bending caused by specific chemical modification, by bound ligands or by the presence of irregular structural elements. We have developed a more rigorous quantitative approach to the analysis of such expe...

Most biological reactions rely on interplay between binding and changes in both macromolecular structure and dynamics. Practical understanding of this interplay requires detection of critical intermediates and determination of their binding and conformational characteristics. However, many of these species are only transiently present and they have often been overlooked in mechanistic studies o...

distribution patterns of ectothermic marine organisms (Fields et al., 1993; Barry et al., 1995; Hughes, 2000). Wholeorganism thermal tolerance limits closely reflect differences in habitat temperature that result from different latitudinal and vertical distribution patterns (Vernberg and Tashian, 1959; Edney, 1961; Stillman and Somero, 1996; Stillman and Somero, 2000; Tomanek and Somero, 2000)....

Properties of supramolecular nanostructures are mediated by conformational, exchange, and water dynamics. Here we review experimental methods recent reports dynamics characterization small molecule nanomaterials.

We analyse the effects of environment (solvent quality, presence extended structures - crowded environment) that may have impact on order transition between denaturated and bounded DNA states lead to changes in scaling laws govern conformational properties strands. find studied significantly influence strength first transition. To this end, we re-consider Poland-Scheraga model apply a polymer f...